[gmx-users] disulfide bond, molecule type

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 28 04:43:48 CEST 2011

Hsin-Lin Chiang wrote:
> Hi,
> I'm trying to heat a protein.
> There are two chains, A-chain and B-chain.
> Two disulfide bonds are between A-chain and B-chain.
> As I know, I should let A-chain and B-chain belong to the same [molecule 
> type] in .top file if I want to have the two inter-bonds.
> So, I delete the TER line between A-chain and B-chain in .pdb file.
> And then I use "pdb2gmx -chainsep interactive" on it .
> I got the two bonds successfully.
> But after heating, the length of A-chain and B-chain in VMD was changed.
> The number of residues in A-chain increase and the ones of B-chain 
> decrease.
> It means some residues move from B-chain to A-chain.
> How should I prevent this kind of error happen.

The labeling changes?  Is this something VMD is doing or something you can 
actually demonstrate in the coordinate file?

> Besides, I found even though I only have protein_A which consist both of 
> A-chain and B-chain.
> The number of first residue of B-chain is started from 1 in .gro file.
> I thought it should be equal to "the number of A-chain's residues plus 1".
> And it was also strange that the number of first water molecules was 
> equal to "the number of B-chain plus 1"
> I thought it should be equal to "the number of A-chain's residues plus 
> the number of B-chain's residues plus 1"
> Is it a bug?

No, it is the expected output.  By default, pdb2gmx does not renumber residues 
consecutively.  This feature was introduced some time ago so that output 
selections could easily be made in multiple chain molecules like this one.  If 
you want residues renumbered consecutively, either post-process the coordinate 
files with genconf -renumber or start over and use pdb2gmx -renum.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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